Updated query parameter binding

Author: davenquinn

services/column-footprint-editor/macrostrat/column_footprint_editor/api/column_groups.py

@@ -24,9 +24,7 @@ async def get(self, request):
 
         if "id" in request.query_params:
             id_ = request.query_params["id"]
-            sql = (
-                "SELECT * FROM ${project_schema}.column_groups WHERE id = " + f"{id_};"
-            )
+            sql = "SELECT * FROM {project_schema}.column_groups WHERE id = " + f"{id_};"
 
             try:
                 df = project.db.exec_query(sql)
@@ -36,7 +34,7 @@ async def get(self, request):
             except error:
                 return JSONResponse({"error": f"col_group {id_} does not exist"})
 
-        sql = """SELECT * from ${project_schema}.column_groups;"""
+        sql = """SELECT * from {project_schema}.column_groups;"""
         try:
             df = project.db.exec_query(sql)
             col_groups = df.to_dict(orient="records")
@@ -49,7 +47,7 @@ async def get(self, request):
     async def post(self, request):
         """Endpoint for new Column Groups"""
 
-        sql = """INSERT INTO ${project_schema}.column_groups(col_group, col_group_name, color)VALUES(
+        sql = """INSERT INTO {project_schema}.column_groups(col_group, col_group_name, color)VALUES(
             :col_group,:col_group_name,:color
         )  """
 
@@ -62,7 +60,7 @@ async def post(self, request):
         try:
             project.db.run_sql(sql, params)
 
-            sql = "SELECT id FROM ${project_schema}.column_groups WHERE col_group = :col_group"
+            sql = "SELECT id FROM {project_schema}.column_groups WHERE col_group = :col_group"
             res = project.db.exec_sql(sql, params=params, count=1)
             params["col_group_id"] = res.id
         except error:
@@ -76,7 +74,7 @@ async def put(self, request):
         """Endpoint for Editing Existing Column Groups"""
 
         sql = """
-            UPDATE ${project_schema}.column_groups cg
+            UPDATE {project_schema}.column_groups cg
                 SET col_group = :col_group,
                 col_group_name = :col_group_name,
                 color = :color

services/column-footprint-editor/macrostrat/column_footprint_editor/api/geometries.py

@@ -202,7 +202,7 @@ async def get_csv(request):
              c.col_group_id,
              c.col_group,
              c.col_group_name
-            from ${project_schema}.column_map_face c; """
+            from {project_schema}.column_map_face c; """
     df = project.db.exec_query(sql)
     csv = df.to_csv()
 

services/column-footprint-editor/macrostrat/column_footprint_editor/database/__init__.py

@@ -1,6 +1,8 @@
-from macrostrat.database import Database as BaseDatabase
-from macrostrat.database.utils import get_sql_text
 from pathlib import Path
+
+from macrostrat.database import Database as BaseDatabase
+from macrostrat.database.utils import get_sql_text, _split_params, _render_query
+from psycopg2.sql import SQL
 from sqlalchemy.orm import sessionmaker
 
 from .sql_formatter import SqlFormatter
@@ -22,6 +24,13 @@
 project_info_insert = procedures / "project-meta-insert.sql"
 project_table = fixtures / "projects_table.sql"
 
+color_description = here / "schema-updates" / "color-description.sql"
+
+
+from macrostrat.utils import get_logger
+
+log = get_logger("uvicorn.error")
+
 
 class Database(BaseDatabase):
     """
@@ -61,6 +70,18 @@ def exec_query(self, filename_or_query, **kwargs):
 
         txt = get_sql_text(filename_or_query)
 
+        params = self.instance_params.copy()
+        for k, v in kwargs.get("params", {}).items():
+            params[k] = v
+
+        # Pre-fill bind parameters
+        params, pre_bind_params = _split_params(params)
+        if pre_bind_params is not None:
+            query = SQL(txt).format(**pre_bind_params)
+            txt = _render_query(query, self.engine)
+
+        kwargs["params"] = params
+        log.info(params)
         return read_sql(txt, self.engine, **kwargs)
 
     #################### db initialization methods ##########################
@@ -113,8 +134,17 @@ def remove_project(self, params={}):
 
     ################## db topology methods ##############################
 
+    def create_topology_tables(self):
+        # Drop topology in case it already exists: (TODO: make this safer)
+        run_topology_command(self, self.project_id, "delete")
+
+        run_topology_command(self, self.project_id, "create_tables")
+
+        # Create color-description tables
+        self.run_sql_file(color_description)
+
     def update_topology(self):
-        run_topology_command(self.project_id, "update")
+        run_topology_command(self, self.project_id, "update")
 
     ###################### Project-Free methods ########################
 

services/column-footprint-editor/macrostrat/column_footprint_editor/database/queries/get-points.sql

@@ -1,5 +1,5 @@
 SELECT
-    ST_AsGeoJSON(point) point,
+    ST_AsGeoJSON(geometry) point,
     id,
     project_id,
     col_id,

services/column-footprint-editor/macrostrat/column_footprint_editor/database/schema-updates/color-description.sql

@@ -1,18 +1,18 @@
--- Add a 'color' column to every column_group table and a 'description' column to every columns table. 
+-- Add a 'color' column to every column_group table and a 'description' column to every columns table.
 -- Loops through each project schema.
 -- Updates the view's for each as well
 
 do $$
-DECLARE 
+DECLARE
 	table_ record;
 BEGIN
 FOR table_ IN
 	SELECT * from pg_tables WHERE tablename LIKE 'column_groups'
 LOOP
 	RAISE info '%.column_groups',table_.schemaname;
 	EXECUTE
-	'ALTER TABLE '|| table_.schemaname ||'.column_groups ADD COLUMN color text;'
-	'ALTER TABLE '|| table_.schemaname ||'.columns ADD COLUMN description text;'
+	'ALTER TABLE '|| table_.schemaname ||'.column_groups ADD COLUMN IF NOT EXISTS color text;'
+	'ALTER TABLE '|| table_.schemaname ||'.columns ADD COLUMN  IF NOT EXISTS description text;'
 	'DROP VIEW IF EXISTS ' || table_.schemaname || '.column_map_face;'
 	'CREATE VIEW ' || table_.schemaname || '.column_map_face AS
 		WITH A as(

services/column-footprint-editor/macrostrat/column_footprint_editor/init_importer.py

@@ -32,7 +32,7 @@ def is_json(myjson):
 # importer.import_column_topology()
 
 # project = Project(10)
-# sql = """ SELECT ST_AsGeoJSON(geometry) polygon, id, project_id, col_id, col_name, col_group_id, col_group, col_group_name, col_color from ${project_schema}.column_map_face c;"""
+# sql = """ SELECT ST_AsGeoJSON(geometry) polygon, id, project_id, col_id, col_name, col_group_id, col_group, col_group_name, col_color from {project_schema}.column_map_face c;"""
 # df = project.db.exec_query(sql)
 
 # cols = df.to_dict(orient="records")

services/column-footprint-editor/macrostrat/column_footprint_editor/project/__init__.py

@@ -1,5 +1,6 @@
-import requests
 from pathlib import Path
+
+import requests
 from psycopg2.sql import Identifier
 
 from mapboard.topology_manager.database import _get_instance_params
@@ -59,7 +60,7 @@ def insert_project_info(self):
 
     def insert_project_column_groups(self):
         route = f"{self.base_url}col_groups?project_id=eq.{self.id}"
-        res = requests.get(route)
+        res = requests.get(route, verify=False)
         data = res.json()
         for column in data:
             params = dict(

services/column-footprint-editor/macrostrat/column_footprint_editor/project/exporter.py

@@ -52,7 +52,7 @@ def export_new_project(self):
         ## insert col-groups get ids and names (need project_id)
         ## use hash-table to store  {col-group-name: col-group-id}
         ## for col insertions
-        col_group_sql = """ SELECT col_group, col_group_name  FROM ${project_schema}.column_groups; """
+        col_group_sql = """ SELECT col_group, col_group_name  FROM {project_schema}.column_groups; """
         col_groups = self.db.exec_sql(col_group_sql)
         col_group_lookup = {}
         for col_group in col_groups:

services/column-footprint-editor/macrostrat/column_footprint_editor/project/importer.py

@@ -30,7 +30,7 @@ def __init__(self, project_id: int, name: str, description: str):
     def get_project_json(self):
         project_id = self.project.id
         url = f"{self.base_url}cols?project_id=eq.{project_id}"
-        res = requests.get(url)
+        res = requests.get(url, verify=False)
         data = res.json()
 
         return data
@@ -65,6 +65,7 @@ def import_column_topology(self):
         self.project.insert_project_column_groups()
         self.columns_import()
         self.db.on_project_insert()
+        self.db.create_topology_tables()
         self.db.update_topology()
         self.db.redump_linework_from_edge()
         self.db.update_topology()

services/column-footprint-editor/macrostrat/column_footprint_editor/settings.py

@@ -1,5 +1,4 @@
 from starlette.config import Config
-from os import path
 
 config = Config(".env")